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Open data
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Basic information
Entry | Database: PDB / ID: 5fxd | ||||||
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Title | Crystal structure of eugenol oxidase in complex with isoeugenol | ||||||
![]() | PROBABLE VANILLYL-ALCOHOL OXIDASE | ||||||
![]() | OXIDOREDUCTASE / BIOCATALYSIS / SELECTIVE OXIDATION / KINETIC RESOLUTION / OXIDASES / EUGENOL | ||||||
Function / homology | ![]() vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / D-lactate dehydrogenase activity / FAD binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nguyen, Q.-T. / de Gonzalo, G. / Binda, C. / Martinez, A.R. / Mattevi, A. / Fraaije, M.W. | ||||||
![]() | ![]() Title: Biocatalytic Properties and Structural Analysis of Eugenol Oxidase from Rhodococcus Jostii Rha1: A Versatile Oxidative Biocatalyst. Authors: Nguyen, Q. / De Gonzalo, G. / Binda, C. / Rioz-Martinez, A. / Mattevi, A. / Fraaije, M.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.6 KB | Display | ![]() |
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PDB format | ![]() | 182.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1015 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 44.8 KB | Display | |
Data in CIF | ![]() | 65.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fxeC ![]() 5fxfC ![]() 5fxpC ![]() 2vaoS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999, 0.02864, -0.03305), Vector: |
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Components
#1: Protein | Mass: 58738.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COVALENT BOND BETWEEN THE FAD AND HIS390 / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Nonpolymer details | FLAVIN-ADENINE DINUCLEOTI | Sequence details | OTHER DETAILS THIS RESEARCH WAS SUPPORTED THE EUROPEAN UNION (EU) PROJECT ROBOX (GRANT AGREEMENT NO. ...OTHER DETAILS THIS RESEARCH WAS SUPPORTED THE EUROPEAN UNION (EU) PROJECT ROBOX (GRANT AGREEMENT NO. 635734) UNDER EU'S HORIZON 2020 PROGRAMME RESEARCH AND INNOVATION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 24% PEG6000, 0.1 M TRIS/HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PILATUS / Detector: PIXEL / Date: Aug 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→85 Å / Num. obs: 109694 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.8 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VAO Resolution: 1.7→89.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.405 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→89.86 Å
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Refine LS restraints |
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